Contacts of the strand formed by residues 42 - 46 (chain M) in PDB entry 6O81
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 42 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M ARG* 5.2 6.6 - - - +
25M SER* 4.9 1.2 + - - -
32M TYR* 3.4 38.1 - - + +
33M VAL 3.4 14.9 - - - +
34M SER* 4.9 5.4 - - - -
35M LEU* 4.5 1.1 - - - -
40M ASN 3.9 2.3 + - - +
41M ILE* 1.3 72.3 - - - +
43M GLY* 1.3 65.7 + - - +
80M GLY 4.8 6.6 - - - +
82M ILE* 3.8 17.2 + - - +
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Residues in contact with GLY 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M TYR* 3.4 7.0 - - - -
33M VAL* 2.9 39.6 + - - +
35M LEU* 4.0 11.8 - - - +
41M ILE 3.6 2.6 + - - -
42M GLU* 1.3 79.6 - - - +
44M MET* 1.3 62.0 + - - +
82M ILE* 3.8 13.7 - - - -
84M LEU* 4.7 0.7 - - - -
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Residues in contact with MET 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F ARG* 2.8 39.3 - - - +
27M ALA* 5.0 0.2 - - + -
29M MET* 4.2 5.8 - - + +
30M GLY 4.0 29.6 - - - +
31M ALA 3.3 5.6 - - - +
32M TYR* 3.6 47.1 - - + +
33M VAL* 4.0 1.4 - - - +
43M GLY* 1.3 74.1 - - - +
45M ILE* 1.3 68.1 + - - +
46M LEU* 3.8 11.1 + - + +
82M ILE 3.1 11.8 + - - +
83M ASP* 3.6 2.7 - - - -
84M LEU* 2.8 33.5 + - - +
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Residues in contact with ILE 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M VAL* 4.2 8.7 - - + -
23M VAL* 5.0 7.0 - - + -
30M GLY* 3.3 1.4 - - - -
31M ALA* 2.9 39.6 + - + +
33M VAL* 3.8 28.0 - - + -
44M MET* 1.3 73.1 - - - +
46M LEU* 1.3 73.0 + - - +
49M GLU 4.8 1.3 - - - +
50M LEU* 4.3 13.7 - - + +
68M GLU* 5.8 1.6 - - + -
70M VAL* 4.2 15.7 - - + -
84M LEU* 3.5 25.8 - - + +
85M SER* 4.3 0.7 - - - -
86M LYS* 4.1 38.4 - - + +
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Residues in contact with LEU 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F ARG* 4.8 5.8 - - - +
29M MET 4.2 6.7 - - - +
30M GLY* 4.4 0.2 - - - -
44M MET* 4.0 26.2 - - + +
45M ILE* 1.3 76.7 - - - +
47M LEU* 1.3 65.3 + - - +
48M SER* 3.3 8.1 - - - +
49M GLU* 3.3 34.2 + - + +
50M LEU* 3.3 16.2 + - - +
73M ILE* 5.9 4.3 - - + -
83M ASP* 4.7 20.4 - - + -
84M LEU 3.3 13.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il